Contradiction with Galatians 1:12
This verse speaks to receiving revelation directly from Jesus Christ, whereas 1 Samuel 3:8 depicts Samuel needing Eli's help to understand God's call.
Galatians 1:12: For I neither received it of man, neither was I taught [it], but by the revelation of Jesus Christ.
Contradiction with Hebrews 1:1
This verse suggests that God spoke in various manners through prophets, contrasting with the direct auditory call to Samuel multiple times.
Hebrews 1:1: God, who at sundry times and in divers manners spake in time past unto the fathers by the prophets,